Peptide validation

The specification development process is a data-driven activity that requires a validated analytical method. The levels of data needed include assay precision, replicate process results (process precision), and real-time stability profiles. A statistical analysis of these data is critical in setting a realistic specification. Most often, aggregation and fragmentation degradation mechanisms are common to protein and peptide therapeutics. Therefore, the SE-HPLC method provides a critical quality parameter that would need to be controlled by a specification limit. 

An important validation of the mice that overexpress human mutant 3APP as a platform for testing therapeutics targeting 3-peptide deposition has been provided by the Elan company, using their PDAPP mouse [146]. Immunization of the mice, either at an early age or after plaques had formed, resulted in clearance of immunoreactive plaques and peptide from the subjects brains. Although the elucidation of the mechanism explaining... 

Capillary zone electrophoresis, an up-to-date high resolution separation method useful for proteins and peptides, has been shown to be a useful method for determining electrophoretic mobilities and diffusion coefficients of proteins [3], Diffusion coefficients can be measured from peak widths of analyte bands. The validity of the method was demonstrated by measuring the diffusion coefficients for dansylated amino acids and myoglobin. 

Although equal amounts of the two possible forms are generated in every synthesis of amino acids, (almost) only L-amino acids are incorporated into proteins and peptides. This phenomenon is valid for the amino acids in all life forms, from the bacterium to the elephant. But there are exceptions some antibiotics contain D-amino acids in their proteins, and these also occur in a few components of cell walls. Here, the D-amino acids have a certain protecting function with respect to degradation enzymes, which are specialised to deal with L-amino acids. 

Bogen S, Vani K, McGraw B, et al. Experimental validation of peptide immunohistochemistry controls. Appl. Immunohistochem. Mol. Morphol. 2009 17 239-246. 

Figure 20.10 Validation by immunohistochemistry of four of the proteins identified in Table 20.1 with single peptide hits. Reproduced with permission from Reference 20. See color insert.

Subsequent to the extensive medicinal chemistry exploration of Orexin antagonism, its utility in the treatment of sleep disorders in man has been reported recently. This important milestone for the therapeutic validation of the target results from the 0X1 /OX2 receptor antagonist ACT-078573 (20) [57], SB-649868 has also been announced to be in phase II clinical development, but neither the structural formula nor the results have been reported to date [58,59]. Moreover, insomnia treatments based on orexin modulation may be addressed by not only receptor antagonism but by inhibition of pathways related to the genesis of the bioactive peptides Orexin A or B, e.g. inhibition of Orexin-converting enzyme [60]. 

The past 3 years have seen tremendous advances in both the design of Cat K inhibitors and in our understanding of the effect of Cat K inhibition on bone remodeling. The structural diversity of Cat K inhibitors has expanded considerably from simple peptidomimetics to non-peptidic derivatives and even non-covalent inhibitors. The potency, selectivity and pharmacokinetic properties of key compounds are very attractive and seem well-suited to further development. The disclosure of clinical validation of the effect of Cat K inhibition on bone mineral density, plus the provocative data suggesting a decoupling of bone resorption and bone formation provides a compelling framework for further development of Cat K inhibitors for the treatment of osteoporosis. 

For reproducible expression analysis and protein quantification MS methods based on isotopic labeling are available. They were designed in conjunction with two or more dimensional chromatographic peptide separation coupled online to MS and require advanced bioinformatics input to analyze the complex data sets in a reasonable time frame. This is also true for the alternative fluorescence-based technology of differential gel electrophoresis (DIGE Fig. 10.6) with tailor-made software which allows statistical validation of multiple data sets. 

If the scope of mass spectrometry is limitless, why are the applications of clinical MS almost completely small molecules The answer is that most clinical tests analyze small molecules, biomarkers that are either metabolites or steroids and, hence, mass spectrometers would target those first. Perhaps a more complete answer would also include that methods must be very robust, easily reproduced in different labs, reliable, and subjected to an extensive array of validation tests. Although peptide and protein analysis is increasing rapidly in clinical labs, the MS approaches to these assays is lagging behind somewhat. MS techniques targeting these peptides and proteins exist, but they are primarily in the research stage, with few systems and methods subjected to the clinical rigors of validation. Once the necessary validations occur and methods simplified, it will only be a short time before MS is used routinely in clinical proteomics. 

J Gerhardt, GJ Nichlson. Validation of a GC-MS method for determination of the optical purity of peptides, in J Martinez, J-A Ferentz, eds. Peptides 2000. Proceedings of the 26th European Peptide Symposium, EDK, Paris, 2001, pp 563-565. 

From the information given above it is obvious that cell surfaces display an enormous complexity. A perfect model to study the interaction of a peptide with a biological membrane would require knowledge about the cell membrane composition in that particular tissue. Even if such information were available it will most probably not be possible to fully mimic the biological environment. However, some important aspects may still be studied with the available models. Whenever possible, one should try to relate the information derived from such a model to information gained from biological data taken on real cells (cell-lines) such as binding affinities etc. in order to prove the validity of the model for the study of a particular aspect. 

Most of the arguments described in the sections on bacterial signal peptides and membrane proteins seem to be valid for the eukaryotic systems, as well as the translocation phenomena across the ER membrane (Sakaguchi, 1997). They seem to be also true for the translocation system across the mitochondrial inner membrane protein into the intermembrane space and the system across the thylakoid membrane in chloroplasts. Although the TAT-dependent pathway has not been found in the ER, it exists on the thylakoid membrane (and possibly on the inner membrane of mitochondria). 

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